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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.14

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-05-10, 01:33 CEST based on data in:

        General Statistics

        Showing 256/256 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        BEB01_1
        35.1%
        49%
        27.0
        BEB01_2
        36.6%
        49%
        27.0
        BEB02_1
        33.5%
        45%
        23.5
        BEB02_2
        33.2%
        45%
        23.5
        BEB03_1
        18.7%
        48%
        27.9
        BEB03_2
        18.9%
        48%
        27.9
        BEB04_1
        18.3%
        48%
        23.9
        BEB04_2
        18.2%
        48%
        23.9
        BEB05_1
        20.4%
        49%
        28.7
        BEB05_2
        20.1%
        49%
        28.7
        BEB10_1
        24.3%
        55%
        23.6
        BEB10_2
        23.8%
        55%
        23.6
        BEB11_1
        25.4%
        51%
        25.5
        BEB11_2
        25.2%
        51%
        25.5
        BEB13_1
        18.7%
        47%
        20.3
        BEB13_2
        18.0%
        47%
        20.3
        BEB15_1
        18.8%
        45%
        22.3
        BEB15_2
        18.3%
        45%
        22.3
        BEB16_1
        26.3%
        44%
        23.1
        BEB16_2
        25.7%
        44%
        23.1
        BEB18_1
        19.3%
        46%
        17.4
        BEB18_2
        18.5%
        46%
        17.4
        BEB19_1
        25.3%
        45%
        23.9
        BEB19_2
        25.0%
        45%
        23.9
        BEB21_1
        26.3%
        43%
        23.8
        BEB21_2
        25.9%
        43%
        23.8
        BEB22_1
        20.3%
        44%
        23.4
        BEB22_2
        20.1%
        44%
        23.4
        BEB23_1
        35.8%
        44%
        23.5
        BEB23_2
        35.5%
        44%
        23.5
        BEB25_1
        12.6%
        46%
        16.4
        BEB25_2
        12.3%
        46%
        16.4
        BEB27_1
        27.5%
        52%
        22.3
        BEB27_2
        27.5%
        52%
        22.3
        BEB28_1
        21.2%
        48%
        22.8
        BEB28_2
        21.4%
        48%
        22.8
        BEB29_1
        28.1%
        52%
        23.5
        BEB29_2
        28.1%
        52%
        23.5
        BEB30_1
        30.4%
        50%
        24.2
        BEB30_2
        30.8%
        50%
        24.2
        BEB31_1
        21.0%
        46%
        24.0
        BEB31_2
        21.1%
        46%
        24.0
        BEB32_1
        35.1%
        45%
        27.0
        BEB32_2
        35.5%
        45%
        27.0
        BEB33_1
        27.8%
        49%
        23.0
        BEB33_2
        28.0%
        49%
        23.0
        BEB34_1
        20.1%
        52%
        21.1
        BEB34_2
        20.5%
        52%
        21.1
        BEN02_1
        42.2%
        47%
        29.3
        BEN02_2
        42.4%
        47%
        29.3
        BEN04_1
        24.4%
        46%
        27.4
        BEN04_2
        24.3%
        46%
        27.4
        BEN05_1
        24.4%
        45%
        27.4
        BEN05_2
        24.6%
        45%
        27.4
        BEN07_1
        19.8%
        46%
        23.3
        BEN07_2
        19.2%
        46%
        23.3
        BEN08_1
        29.7%
        45%
        28.5
        BEN08_2
        29.2%
        45%
        28.5
        BEN09_1
        20.9%
        47%
        27.0
        BEN09_2
        20.3%
        47%
        27.0
        BEN10_1
        51.1%
        47%
        26.2
        BEN10_2
        50.8%
        47%
        26.2
        BEN11_1
        27.5%
        45%
        26.6
        BEN11_2
        27.1%
        45%
        26.6
        BEN12_1
        33.5%
        46%
        28.2
        BEN12_2
        33.3%
        46%
        28.2
        BEN13_1
        23.8%
        45%
        26.0
        BEN13_2
        23.6%
        45%
        26.0
        BEN14_1
        21.3%
        45%
        26.9
        BEN14_2
        20.3%
        46%
        26.9
        BEN16_1
        34.8%
        46%
        27.2
        BEN16_2
        32.7%
        46%
        27.2
        BEN17_1
        24.4%
        45%
        28.0
        BEN17_2
        23.2%
        45%
        28.0
        BEN18_1
        30.2%
        45%
        27.9
        BEN18_2
        28.7%
        45%
        27.9
        BEN19_1
        31.1%
        44%
        24.3
        BEN19_2
        29.3%
        44%
        24.3
        BEN20_1
        23.7%
        46%
        26.3
        BEN20_2
        22.5%
        46%
        26.3
        BEN21_1
        21.9%
        45%
        28.0
        BEN21_2
        20.5%
        45%
        28.0
        BEN22_1
        25.9%
        46%
        25.9
        BEN22_2
        25.0%
        46%
        25.9
        BEN23_1
        37.0%
        46%
        27.2
        BEN23_2
        34.9%
        46%
        27.2
        BEN24_1
        27.8%
        46%
        25.3
        BEN24_2
        26.3%
        46%
        25.3
        BEN26_1
        17.8%
        49%
        20.8
        BEN26_2
        18.3%
        49%
        20.8
        BEN27_1
        37.8%
        47%
        23.9
        BEN27_2
        38.1%
        47%
        23.9
        BEN28_1
        17.0%
        46%
        24.0
        BEN28_2
        17.5%
        46%
        24.0
        BEN29_1
        49.2%
        47%
        25.9
        BEN29_2
        49.7%
        47%
        25.9
        BEN30_1
        31.6%
        46%
        24.3
        BEN30_2
        32.2%
        46%
        24.3
        BEN31_1
        24.6%
        47%
        21.7
        BEN31_2
        25.2%
        47%
        21.7
        BEN32_1
        25.0%
        45%
        23.8
        BEN32_2
        25.6%
        45%
        23.8
        BEN33_1
        21.4%
        46%
        25.7
        BEN33_2
        21.6%
        46%
        25.7
        BEN34_1
        13.9%
        49%
        23.4
        BEN34_2
        14.2%
        49%
        23.4
        BEN35_1
        43.2%
        44%
        30.0
        BEN35_2
        43.4%
        43%
        30.0
        BEN36_1
        24.9%
        46%
        26.1
        BEN36_2
        25.2%
        46%
        26.1
        BEN37_1
        23.0%
        46%
        9.0
        BEN37_2
        23.1%
        46%
        9.0
        BEN38_1
        26.1%
        46%
        24.7
        BEN38_2
        26.3%
        46%
        24.7
        BEN39_1
        17.4%
        47%
        25.3
        BEN39_2
        17.3%
        47%
        25.3
        BEN40_1
        22.0%
        46%
        26.9
        BEN40_2
        21.9%
        46%
        26.9
        BEN41_1
        30.4%
        46%
        23.9
        BEN41_2
        30.3%
        46%
        23.9
        BEN42_1
        30.8%
        44%
        22.3
        BEN42_2
        30.9%
        44%
        22.3
        BEN43_1
        21.3%
        47%
        26.5
        BEN43_2
        21.4%
        47%
        26.5
        BEN44_1
        30.9%
        46%
        25.8
        BEN44_2
        30.7%
        46%
        25.8
        BEN45_1
        18.9%
        48%
        24.1
        BEN45_2
        18.7%
        48%
        24.1
        BEN46_1
        38.6%
        46%
        26.3
        BEN46_2
        38.3%
        46%
        26.3
        BEN47_1
        20.9%
        47%
        23.7
        BEN47_2
        20.7%
        47%
        23.7
        BEN49_1
        21.3%
        47%
        21.8
        BEN49_2
        21.0%
        47%
        21.8
        BEN50_1
        23.3%
        44%
        21.5
        BEN50_2
        23.3%
        44%
        21.5
        BEN51_1
        25.7%
        44%
        21.3
        BEN51_2
        25.4%
        44%
        21.3
        BEN52_1
        31.7%
        45%
        23.4
        BEN52_2
        31.9%
        45%
        23.4
        BEN53_1
        23.9%
        46%
        19.7
        BEN53_2
        24.0%
        46%
        19.7
        BEN54_1
        26.2%
        45%
        21.6
        BEN54_2
        26.3%
        45%
        21.6
        BEN55_1
        14.6%
        47%
        20.9
        BEN55_2
        14.6%
        47%
        20.9
        BEN56_1
        12.8%
        47%
        13.8
        BEN56_2
        12.2%
        47%
        13.8
        BEN57_1
        19.4%
        46%
        20.1
        BEN57_2
        18.8%
        46%
        20.1
        BEN58_1
        17.5%
        47%
        18.4
        BEN58_2
        17.1%
        47%
        18.4
        BEN60_1
        30.5%
        45%
        24.2
        BEN60_2
        30.0%
        45%
        24.2
        BEN61_1
        21.8%
        45%
        22.4
        BEN61_2
        21.2%
        45%
        22.4
        BEN62_1
        21.6%
        48%
        19.1
        BEN62_2
        21.1%
        48%
        19.1
        BEN63_1
        20.0%
        45%
        21.8
        BEN63_2
        19.6%
        45%
        21.8
        BEN64_1
        29.3%
        46%
        21.9
        BEN64_2
        29.3%
        46%
        21.9
        BEN65_1
        19.5%
        48%
        20.7
        BEN65_2
        19.2%
        48%
        20.7
        BEN66_1
        21.6%
        45%
        19.0
        BEN66_2
        21.3%
        45%
        19.0
        BEN69_1
        29.8%
        45%
        22.1
        BEN69_2
        29.0%
        45%
        22.1
        BEN70_1
        15.3%
        47%
        17.5
        BEN70_2
        15.1%
        47%
        17.5
        BEN71_1
        33.8%
        46%
        20.7
        BEN71_2
        33.3%
        46%
        20.7
        BEN72_1
        17.0%
        49%
        19.9
        BEN72_2
        16.9%
        49%
        19.9
        BEN73_1
        21.7%
        46%
        23.3
        BEN73_2
        21.3%
        46%
        23.3
        BEN74_1
        30.4%
        46%
        25.6
        BEN74_2
        30.0%
        46%
        25.6
        BEN75_1
        23.2%
        44%
        20.9
        BEN75_2
        23.0%
        44%
        20.9
        BEN76_1
        18.6%
        44%
        20.2
        BEN76_2
        18.9%
        44%
        20.2
        BEN77_1
        25.9%
        44%
        22.9
        BEN77_2
        25.7%
        44%
        22.9
        BEN78_1
        35.2%
        45%
        21.6
        BEN78_2
        35.0%
        45%
        21.6
        BEN80_1
        29.6%
        45%
        21.1
        BEN80_2
        30.0%
        45%
        21.1
        BEN81_1
        22.0%
        46%
        23.1
        BEN81_2
        22.0%
        46%
        23.1
        BEN82_1
        37.7%
        45%
        22.6
        BEN82_2
        37.7%
        45%
        22.6
        BEY01_1
        19.4%
        47%
        26.1
        BEY01_2
        19.8%
        47%
        26.1
        BEY02_1
        31.0%
        48%
        25.9
        BEY02_2
        31.2%
        48%
        25.9
        BEY03_1
        23.9%
        48%
        26.4
        BEY03_2
        24.3%
        48%
        26.4
        BEY04_1
        19.8%
        49%
        28.1
        BEY04_2
        19.8%
        49%
        28.1
        BEY05_1
        35.6%
        49%
        25.8
        BEY05_2
        35.4%
        49%
        25.8
        BEY06_1
        30.9%
        45%
        26.5
        BEY06_2
        30.3%
        45%
        26.5
        BEY07_1
        19.9%
        51%
        27.2
        BEY07_2
        19.6%
        51%
        27.2
        BEY08_1
        22.5%
        48%
        24.7
        BEY08_2
        22.0%
        48%
        24.7
        BEY09_1
        19.6%
        51%
        22.8
        BEY09_2
        19.6%
        51%
        22.8
        BEY10_1
        18.7%
        53%
        21.9
        BEY10_2
        18.6%
        53%
        21.9
        BEY11_1
        32.7%
        50%
        25.6
        BEY11_2
        32.4%
        50%
        25.6
        BEY12_1
        32.5%
        50%
        28.0
        BEY12_2
        32.5%
        50%
        28.0
        BEY13_1
        29.6%
        44%
        20.1
        BEY13_2
        29.8%
        44%
        20.1
        BEY14_1
        29.1%
        46%
        21.5
        BEY14_2
        28.8%
        46%
        21.5
        BEY15_1
        27.6%
        45%
        24.7
        BEY15_2
        27.9%
        45%
        24.7
        BEY16_1
        26.3%
        47%
        21.0
        BEY16_2
        26.3%
        47%
        21.0
        BEY17_1
        35.1%
        45%
        25.2
        BEY17_2
        35.1%
        45%
        25.2
        BEY18_1
        40.4%
        45%
        22.6
        BEY18_2
        40.4%
        45%
        22.6
        BEY19_1
        18.6%
        47%
        22.2
        BEY19_2
        18.5%
        47%
        22.2
        BEY20_1
        21.6%
        45%
        22.1
        BEY20_2
        21.2%
        45%
        22.1
        BEY21_1
        28.5%
        46%
        24.0
        BEY21_2
        28.4%
        46%
        24.0
        BEY22_1
        25.8%
        47%
        23.3
        BEY22_2
        25.7%
        47%
        23.3
        BEY23_1
        22.0%
        46%
        25.4
        BEY23_2
        21.9%
        46%
        25.4
        BEY24_1
        19.4%
        49%
        20.1
        BEY24_2
        19.3%
        49%
        20.1
        BEY25_1
        20.5%
        47%
        22.2
        BEY25_2
        20.5%
        47%
        22.2
        BEY26_1
        21.6%
        53%
        22.4
        BEY26_2
        21.1%
        53%
        22.4
        BEY27_1
        19.1%
        49%
        23.1
        BEY27_2
        19.3%
        49%
        23.1
        BEY28_1
        25.8%
        52%
        23.2
        BEY28_2
        25.8%
        52%
        23.2
        BEY29_1
        18.8%
        50%
        22.8
        BEY29_2
        18.8%
        50%
        22.8
        BEY30_1
        19.9%
        51%
        21.2
        BEY30_2
        18.9%
        51%
        21.2
        BEY31_1
        15.2%
        50%
        20.9
        BEY31_2
        15.4%
        50%
        20.9
        BEY32_1
        28.1%
        47%
        23.5
        BEY32_2
        27.9%
        47%
        23.5

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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        Sequence Length Distribution

        All samples have sequences of a single length (126bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        256 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.